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path: root/gn3/api/metadata.py
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2024-04-30Add docstring to view_history function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Use JWT tokens from gn-auth.Munyoki Kilyungi
* gn3/api/metadata.py: Import time, jwt, AUthorisationError. (edit_dataset): Use JWT tokens from gn-auth and validate them. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Add an endpoint to query a dataset's git history from it's id.Munyoki Kilyungi
* gn3/api/metadata.py: Import get_history. (view_history): New endpoint. * gn3/db/datasets.py (get_history): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Rename retrieve_dataset_metadata to retrieve_metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-15Use correct names for dataset entries in json result.Munyoki Kilyungi
Since we are appending to an already flattened json-ld file, we don't need to add the prefixes. * gn3/api/metadata.py (DATASET_CONTEXT): Add missing "experimentType" key. * gn3/db/datasets.py (retrieve_dataset_metadata): Match the __subject dict with entries from DATASET_CONTEXT. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-14Remove try ... except clauses around RDF endpoints.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-14Stem the dataset's id before constructing the path.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-13Use correct path for dataset metadata files.Munyoki Kilyungi
* gn3/api/metadata.py (datasets): Use "gn-docs/general/datasets". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-13Update "dataset/<name>" API endpoint to fetch metadata from files.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-10Optionally fetch dataset metadata if provided during genotype fetch.Munyoki Kilyungi
* gn3/api/metadata.py (genotypes): If a dataset name is provided fetch the group it belongs to and the dataset's full and short name. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-10Switch to gnt:belongsToSpecies in genotype queries.Munyoki Kilyungi
* gn3/api/metadata.py (genotypes): Use gnt:belongsToSpecies instead of xkos:classifiedUnder when querying for species. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-10Remove hard-coded dataset name.Munyoki Kilyungi
* gn3/api/metadata.py (probesets): Remove hard-coded "HC_M2_0606_P" in probeset RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-08Optionally fetch dataset metadata if provided during probeset fetch.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Remove extra gene metadata from query as it's un-necessary.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Add extra keys to the Probeset's json-ld context.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Refactor gene symbol handling and add references to probeset.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Use gnt:geneSymbol property to fetch genes in Probeset RDF query.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Update RDF ProbeSet query.Munyoki Kilyungi
* gn3/api/metadata.py (probesets): Update RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15First frame and then compact probeset results.Munyoki Kilyungi
* gn3/api/metadata.py: Reshape the data in a nice way by first framing and compacting the json-ld result. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Update ProbeSet's context.Munyoki Kilyungi
* gn3/api/metadata.py (probesets): Update context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Update BASE_CONTEXT entries.Munyoki Kilyungi
* gn3/api/metadata.py: (PHENOTYPE_CONTEXT): Move "rdfs", "gnt", "gnc"... (BASE_CONTEXT): ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Fix typo in GoTree prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Add optional property for platform info in dataset representation.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Fetch normalization metadata correctly.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Fix typo in platform prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Refactor metadata mappings for improved dataset representation.Munyoki Kilyungi
* gn3/api/metadata.py: (DATASET_CONTEXT): Remove "ex:" prefixes. Add new prefixes for citation, platform, GoTree, tissueInfo, contactWebUrl and contactName. (datasets): Update query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Update phenotype queries to use gnt:belongsToGroup.Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Use gnt:belongsToGroup instead of xkos:classifiedUnder. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Add a phenotype's chromosome location to the Phenotype fetch.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Place publication details on a sub-graph of its own.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Replace LRS with lodScore.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Remove unused variable "args".Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Delete "args". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Attach phenotype endpoints to one function.Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Add "/phenotypes/<group>/<name>" to this endpoint. (fetch_phenotype_by_group): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Use "dcat:Dataset" when framing when fetching phenotypes.Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Filter for "dcat:Dataset" in json-ld context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Construct a more semantic graph for phenotypes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Remove unused argument during template substitution.Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Delete "name" from template substitution. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Replace "ex:" prefix with a semantic prefix when fetching phenotype.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Add "gnt:abbreviation" and "ex:inbredSet" to PHENOTYPE_CONTEXT.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Add "ex:species" to phenotypes json-ld context.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Return distinct results after a dataset search.Munyoki Kilyungi
* gn3/api/metadata.py (search_datasets): Return distinct search results. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Add ex:pages and ex:hits to the search context.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27First fram and compact the jsonld results during dataset search.Munyoki Kilyungi
* gn3/api/metadata.py (search_datasets): Replace query_and_frame with query_frame_and_compact. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Add "inbredSet" to the dataset's search context.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Fetch a dataset's contributors in RDF.Munyoki Kilyungi
* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "contributors." (datasets): Fetch a dataset's contributors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Fetch dataset specifics in RDF.Munyoki Kilyungi
* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "specifics". (datasets): Fetch a dataset's specifics. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Refactor to use new rdf.query_* abstractions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Fix pylint error.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Refactor to use new rdf.query_* abstractions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Make implicit optional type hints PEP 484 compliant.Munyoki Kilyungi
Ran the command: pipx run no_implicit_optional ./ in the root directory.
2023-10-27Abstract out (sparql) CONSTRUCT into a function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Delete unused imports.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 07:47:24 +0000